Breath-by-breath measurements of end-tidal O₂ and CO₂ concentrations in harbor porpoise reveal that the respiratory gas exchange ratio (R_R; CO₂ output/O₂ uptake) of the first lung ventilation in a breathing bout after a prolonged breath-hold is always well below the animal's metabolic respiratory quotient (RQ) of 0.85. Thus the longest apneic pauses are always followed by an initial breath having a very low R_R (0.6-0.7), which thereafter increases with each subsequent breath to values in excess of 1.2. Although the O₂ stores of the body are fully readjusted after the first three to four breaths following a prolonged apneic pause, a further three to four ventilations are always needed, not to load more O₂ but to eliminate built-up levels of CO₂. The slower readjustment of CO₂ stores relates to their greater magnitude and to the fact that they must be mobilized from comparatively large and chemically complex HCO/CO₂ stores that are built up in the blood and tissues during the breath-hold. These data, and similar measurements on gray seals (12), indicate that it is the readjustment of metabolic RQ and not O₂ stores per se that governs the amount of time an animal must spend ventilating at the surface after a dive.